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Inorganic chemistry
B.Sc III
Bioinorganic chemistry
Inorganic Elements in Biological Systems
– Bulk Elements: O, C, H, N, Ca, S, P,
Na, K, Cl, Mg, etc.
• Trace Elements: Mo, Mn, Fe, Co, Cu,
Zn, I, Si, etc.
• Ultra-trace Elements: V, Cr, Se, Br, Sn,
F, etc.
Porphyrins and Related Complexes in
Bioinorganic Molecules
• A porphine ring has a square planar geometry with a
“pocket” in the center.
• A metalloporphyrin complex can result by
incorporating a metal atom into the pocket (look at
heme from Rasmol).
– Axial sites are available for other ligands.
• Structure, specificity, and reactivity are changed by
differing the side chains, metal ions, and surrounding
species.
Porphyrins
Metalloporphyrin complex
Heme B group of hemoglobin. An iron (Fe) atom in the middle is shown in red,
complexed to four interior nitrogen atoms shown in blue.
Hemoglobin and Myoglobin
• Oxygen transfer and storage agents in the
blood and muscle tissue.
– Hemoglobin transports oxygen (O2) from the
lungs/gills to tissues and muscles.
– Myoglobin stores oxygen (O2) in the muscles and
tissues.
Oxygen commonly transfers from the hemoglobin to
the myoglobin for later use.
Hemoglobin (I)
• Made up of four globin protein subunits ( and ).
– Each protein partially encloses a heme group.
• Each heme group is in a porphyrin pocket.
– One axial position of the iron is bound to an imidazole
nitrogen from the protein.
– One axial position is available/vacant or has H2O bound
to it.
• Dissolved O2 can bind reversibly to this axial position.
http://www.umass.edu/microbio/chime/hemoglob/
Hemoglobin (II)
• In hemoglobin, the Fe(II) does not become
oxidized to Fe(III) or Fe(IV).
– Occurs readily in simpler systems (see Figure on the
next page).
• There needs to be reversible binding of the O2
without oxidation. A free heme also oxidizes in
an aqueous environment.
– Why doesn’t oxidation occur in hemoglobin by O2
or H2O?
Hemoglobin (Figures)
Hemoglobin (III)
• In nonoxygenated hemoglobin, the Fe(II) is about 70
pm out of the plane of the porphyrin nitrogens
(show with Chime).
• Bonding O2 or CO in the sixth position causes the
iron to be come planar.
– Fe(II) becomes diamagnetic
• Oxygen bonds at an angle of ~130 degrees (show
with Chime).
Explain these structural changes upon bonding.
Hemoglobin(IV)
• There is a considerable amount of 
backbonding from the metal to the O2.
– Can be described as Fe(III)-O2-
• Why is the O2 bent? The energy changes very
little with this angle.
– suggestions
Hemoglobin (V)
• Cooperativity
– The function of hemoglobin is to bind O2 at high oxygen
pressure and carry it through the blood to needed areas
(and myoglobin for storage).
Hb + 4O2  Hb(O2)4
Hb(O2)4 + 4Mb  4Mb(O2) + Hb
• As one iron binds an oxygen molecule in Hb, the
molecular shape changes to make binding of
additional oxygen molecules easier. In a similar
fashion, initial removal of oxygen triggers the release
of the remaining oxygens.
Hemoglobin
• At low partial pressures of
O2, Mb has a much greater
affinity for O2.
K Mb 
[Mb(O 2 )]
[Mb][O 2 ]
K Hb 
[Hb (O 2 ) 4 ]
[Hb ][O 2 ]2.8
• The Bohr effect.
– Increased acidity favors the
release of O2 from Hb(O2)4
Biological Role of Sodium
Sodium is important in the body, as it helps maintain body fluid
homeostasis. People with disorders that do not have enough sodium in the
body can take medication such as serum sodium in order to maintain a healthy
amount of sodium in the body. Sodium is also crucial in osmotic pressure, as
the body adjusts to when there is too little or too much sodium in the
body. Sodium is also the main cation in outside cells containing fluid in
mammalian bodies, and very little sodium inside the cells, consisting of
approximately 90% of the body's total sodium content.
Biological Role of Magnesium and calcium
Magnesium and calcium are ubiquitous and essential to all known living organisms.
They are involved in more than one role, with, for example, Mg/Ca ion pumps
playing a role in some cellular processes, magnesium functioning as the active
center in some enzymes, and calcium salts taking a structural role
Nitrogen Fixation
• The growth of all organisms depend on the
availability of Nitrogen (e.g. amino acids)
• Nitrogen in the form of Dinitrogen (N2) makes
up 80% of the air we breathe but is
essentially inert due to the triple bond (NN)
• In order for nitrogen to be used for growth it
must be "fixed" (combined) in the form of
ammonium (NH4) or nitrate (NO3) ions.
Nitrogen Fixation
• The nitrogen molecule
(N2) is quite inert. To
break it apart so that
its atoms can combine
with other atoms
requires the input of
substantial amounts of
energy.
• Three processes are
responsible for most
of the nitrogen
fixation in the
biosphere:
• atmospheric fixation
• biological fixation
• industrial fixation
Biological Fixation cont.
•
Biological nitrogen fixation requires a complex set of enzymes and a huge
expenditure of ATP.
•
Although the first stable product of the process is ammonia, this is quickly
incorporated into protein and other organic nitrogen compounds.
•
Scientist estimate that biological fixation globally adds approximately 140
million metric tons of nitrogen to ecosystems every year.
Some nitrogen fixing organisms
• Free living aerobic bacteria
– Azotobacter
– Beijerinckia
– Klebsiella
– Cyanobacteria (lichens)
• Free living associative bacteria
– Azospirillum
• Free living anaerobic bacteria
• Symbionts
– Clostridium
– Rhizobium (legumes)
– Desulfovibrio
– Frankia (alden trees)
– Purple sulphur bacteria
– Purple non-sulphur bacteria
– Green sulphur bacteria
Some nitrogen fixing organisms
Free living
Symbiotic
Aerobes
Anaerobes
Leguminous Non
Heterotrophs
Phototrophs Heterotrophs Phototrophs plants
leguminous plants
Azotobacter spp. Various
Clostridium spp Chromatium
soybeans,
Alnus, Myrica
Klebsiella
Cyanobacteria Desulfovibrio Chloribium
clover,
Ceanthus
Beijerinckia
DisulfotoRhodospirillum locust, etc
Comptorinia
Bacillus
maculum
Rhodopseudo- In association Casurina
polymyxa
monas
with a bacterium in assocation
Mycobacterium
Rhodoof the genus
with
flavum
microbium Rhizobium or actinomycetes
Azospirillium
Rhodobacter Bradyrhizobium of the genus
lipoferum
Heliobacterium
Frankia
Citrobacter
freundii
Some
Methylotrophs
Nitrogen Fixation
• All nitrogen fixing bacteria use highly conserved
enzyme complex called Nitrogenase
• Nitrogenase is composed of of two subunits: an
iron-sulfur protein and a molybdenum-iron-sulfur
protein
• Aerobic organisms face special challenges to
nitrogen fixation because nitrogenase is
inactivated when oxygen reacts with the iron
component of the proteins
Nitrogenase
FeMo Cofactor
Fd(ox)
N2 + 8H+
Fd(red)
8e-
2NH3 + H2
nMgATP
nMgADP + nPi
Dinitrogenase
reductase
4C2H2 + 8H+
4C2H2
Dinitrogenase
N2 + 8H+ + 8e- + 16 MgATP  2NH3 + H2 + 16MgADP
Nitrogenase
Types of Biological Nitrogen Fixation
Free-living (asymbiotic)
• Cyanobacteria
• Azotobacter
Associative
• Rhizosphere–Azospirillum
• Lichens–cyanobacteria
• Leaf nodules
Symbiotic
• Legume-rhizobia
• Actinorhizal-Frankia